Dix-seq: An integrated pipeline for fast amplicon data analysis
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GRAPHICAL ABSTRACT
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PUBLIC SUMMARY
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An integrated pipeline for optimized amplicon analysis has been developed.
Dix-seq offers a one-step process with a single parameter sheet file to complete the entire pipeline.
The modular design of Dix-seq supports custom analysis.
Retrospective scripts make reproducing results or debugging errors easy.
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ABSTRACT
Rapid advancements in sequencing technologies in the past decade have driven the widespread adoption of amplicon metagenome. However, current amplicon data analysis software/pipelines often require manual intervention spanning multiple steps, necessitating a clear understanding of parameters and hindering inexperienced users from automating their workflows. Here, we introduce Dix-seq, a fully containerized tool for rapid, automated, and scalable amplicon data analysis. With one single command, Dix-seq can process raw amplicon sequences down to various statistical and visualization results, generate html-based reports, and retrospective logfiles. Dix-seq utilizes a single parameter sheet file to drastically simplify its command line interface, making it much more approachable by inexperienced users while improving study reproducibility. The modular design of Dix-seq enables rapid adoption of new methods and databases into its software frame. Currently, more than 21 algorithms, software, and third-party procedures have been integrated into eight modules in Dix-seq, while more are coming down the line. This approach also allows experienced users to fine-tune the workflow, facilitating customized analysis. Benchmarks performed on datasets from real-world case studies demonstrated Dix-seq’s capabilities in generating publish-ready figures integrated with statistical information and extracting biologically meaningful patterns. Furthermore, it remained highly effective at detecting variance upon simulated sequencing depth drop, the results remained robust down to a depth of11000 and1000 in all and certain fronts, such as phylogenetic diversity and Pearson correlation, respectively. In summary, Dix-seq is a convenient yet highly customizable tool for amplicon data analysis, making it an ideal choice for both entry-level and experienced users. -
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Cite this article:
Dong P., Chen Y., Wei Y., et al. (2025). Dix-seq: An integrated pipeline for fast amplicon data analysis. The Innovation Life 3:100120. https://doi.org/10.59717/j.xinn-life.2024.100120
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Dong P., Chen Y., Wei Y., et al. (2025). Dix-seq: An integrated pipeline for fast amplicon data analysis. The Innovation Life 3:100120. https://doi.org/10.59717/j.xinn-life.2024.100120
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Figure 1.
Dix-seq: An integrated pipeline for fast amplicon data analysis
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Figure 2.
Analysis and visualization results of Study I (environmental microbiome) reveal differentiation of microbial species (ZOTUs) and function (KOs) across estuary zones by using one-step workflows “pipeline, advanced” in dix-seq
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Figure 3.
Examples of publication-quality visualization results of Study I by using step-by-step mode with “DESeq2, picrust2, keeg” subcommand combination in dix-seq
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Figure 4.
Comparison of runtime, taxonomic annotations, and alpha diversity indexes on the data set of Study II (Wang et al.) using alternative protocols
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Figure 5.
Procrustes analysis showed the correlation between the composition previously reported in Study II (Wang et al.) and the results of alternative protocols
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Figure 6.
Comparison of beta diversity analysis results on the data set of Study II using alternative protocols
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Figure 7.
Impact of sequencing depth on the result of the Dix-seq software
